High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs.

Reverse transcription of the HIV-1 viral RNA genome (vRNA) is an integral step in virus replication. Upon viral entry, HIV-1 reverse transcriptase (RT) initiates from a host tRNALys3 primer bound to the vRNA genome and is the target of key antivirals, such as non-nucleoside reverse transcriptase inhibitors (NNRTIs). Initiation proceeds slowly with discrete pausing events along the vRNA template. Despite prior medium-resolution structural characterization of reverse transcriptase initiation complexes (RTICs), higher-resolution structures of the RTIC are needed to understand the molecular mechanisms that underlie initiation. Here we report cryo-EM structures of the core RTIC, RTIC-nevirapine, and RTIC-efavirenz complexes at 2.8, 3.1, and 2.9 Å, respectively. In combination with biochemical studies, these data suggest a basis for rapid dissociation kinetics of RT from the vRNA-tRNALys3 initiation complex and reveal a specific structural mechanism of nucleic acid conformational stabilization during initiation. Finally, our results show that NNRTIs inhibit the RTIC and exacerbate discrete pausing during early reverse transcription.

Covalent Histone Modification by an Electrophilic Derivative of the Anti-HIV Drug Nevirapine.

Nevirapine (NVP), a non-nucleoside reverse transcriptase inhibitor widely used in combined antiretroviral therapy and to prevent mother-to-child transmission of the human immunodeficiency virus type 1, is associated with several adverse side effects. Using 12-mesyloxy-nevirapine, a model electrophile of the reactive metabolites derived from the NVP Phase I metabolite, 12-hydroxy-NVP, we demonstrate that the nucleophilic core and C-terminal residues of histones are targets for covalent adduct formation. We identified multiple NVP-modification sites at lysine (e.g., H2BK47, H4K32), histidine (e.g., H2BH110, H4H76), and serine (e.g., H2BS33) residues of the four histones using a mass spectrometry-based bottom-up proteomic analysis. In particular, H2BK47, H2BH110, H2AH83, and H4H76 were found to be potential hot spots for NVP incorporation. Notably, a remarkable selectivity to the imidazole ring of histidine was observed, with modification by NVP detected in three out of the 11 histidine residues of histones. This suggests that NVP-modified histidine residues of histones are prospective markers of the drug's bioactivation and/or toxicity. Importantly, NVP-derived modifications were identified at sites known to determine chromatin structure (e.g., H4H76) or that can undergo multiple types of post-translational modifications (e.g., H2BK47, H4H76). These results open new insights into the molecular mechanisms of drug-induced adverse reactions.

Molecular Recognition of the HPLC Whelk-O1 Selector towards the Conformational Enantiomers of Nevirapine and Oxcarbazepine.

The presence of stereogenic elements is a common feature in pharmaceutical compounds, and affording optically pure stereoisomers is a frequent issue in drug design. In this context, the study of the chiral molecular recognition mechanism fundamentally supports the understanding and optimization of chromatographic separations with chiral stationary phases. We investigated, with molecular docking, the interactions between the chiral HPLC selector Whelk-O1 and the stereoisomers of two bioactive compounds, the antiviral Nevirapine and the anticonvulsant Oxcarbazepine, both characterized by two stereolabile conformational enantiomers. The presence of fast-exchange enantiomers and the rate of the interconversion process were studied using low temperature enantioselective HPLC and VT-NMR with Whelk-O1 applied as chiral solvating agent. The values of the energetic barriers of interconversion indicate, for the single enantiomers of both compounds, half-lives sufficiently long enough to allow their separation only at critically sub-ambient temperatures. The chiral selector Whelk-O1 performed as a strongly selective discriminating agent both when applied as a chiral stationary phase (CSP) in HPLC and as CSA in NMR spectroscopy.

Photocatalytic degradation of nevirapine with a heterostructure of few-layer black phosphorus coupled with niobium (V) oxide nanoflowers (FL-BP@Nb2O5).

The degradation and removal of antiviral drugs in water has emerged remains a major challenge. This work presents, the photodegradation of nevirapine (NVP) with a novel p-n heterostructure of FL-BP@Nb2O5 nanoparticles synthesized via hydrothermal method. Several characterization techniques revealed a successful formation of the heterostructure with well aligned band positions that promoted excellent separation of charge carriers. A systematic study was conducted on the effect of initial pH, initial catalyst loading and initial concentration on the degradation kinetics of NVP. Degradation efficiency of 68% was achieved with the FL-BP@Nb2O5 after 3 h with 5 ppm initial concentration solution of NVP, at a working pH of 3 and 15 mg of photocatalyst. The stable fragment resulting from the degradation of NVP was n-butanol as evidenced by LC/MS. The successful degradation of NVP transpired with synergistic effect exhibited by the heterostructure that led to accelerated formation of reactive species that were responsible for the breaking down of NVP into smaller fragments. A TOC removal percentage of 19.03% after the photodegradation of NVP was observed, suggesting a successful break down of NVP to simpler non-toxic carbon-containing compounds.

Molecular Docking Studies and Synthesis of Amino-oxy-diarylquinoline Derivatives as Potent Non-nucleoside HIV-1 Reverse Transcriptase Inhibitors.

In this study, amino-oxy-diarylquinolines were designed using structure-guided molecular hybridization strategy and fusing of the pharmacophore templates of nevirapine (NVP), efavirenz (EFV), etravirine (ETV, TMC125) and rilpivirine (RPV, TMC278). The anti-HIV-1 reverse transcriptase (RT) activity was evaluated using standard ELISA method, and the cytotoxic activity was performed using MTT and XTT assays. The primary bioassay results indicated that 2-amino-4-oxy-diarylquinolines possess moderate inhibitory properties against HIV-1 RT. Molecular docking results showed that 2-amino-4-oxy-diarylquinolines 8(A-D): interacted with the Lys101 and His235 residue though hydrogen bonding and interacted with Tyr318 residue though π-π stacking in HIV-1 RT. Furthermore, 8A: and 8D: were the most potent anti-HIV agents among the designed and synthesized compounds, and their inhibition rates were 34.0% and 39.7% at 1 µM concentration. Interestingly, 8A: was highly cytotoxicity against MOLT-3 (acute lymphoblastic leukemia), with an IC50 of 4.63±0.62 µg/mL, which was similar with that in EFV and TMC278 (IC50 7.76±0.37 and 1.57±0.20 µg/ml, respectively). Therefore, these analogs of the synthesized compounds can serve as excellent bases for the development of new anti-HIV-1 agents in the near future.

A personally guided tour on some of our data with the Ames assay-A tribute to Professor Bruce Ames.

In contributing to this Special Issue of Mutation Research dedicated to Professor Bruce N. Ames in recognition of his 90th birthday in December 2018, we intend to portray the importance not only of the Ames Salmonella/mammalian-microsome mutagenicity assay in some of our studies over the years, but also the importance of the insight that Bruce Ames brought to the field of genetic toxicology.

Amorphous solid dispersions of weak bases with pH-dependent soluble polymers to overcome limited bioavailability due to gastric pH variability - An in-vitro approach.

Several drugs are pH-dependent soluble weak bases with a poor solubility in the intestinal pH range. Additionally a variable gastric pH, which is a common issue in the population, potentially reduces the in-vivo performance due to reduced solubility at elevated pH. Aiming to avoid the influence of variable gastric pH on the dissolution performance, enteric polymers - hydroxypropylmethylcellulose acetate succinate (HPMCAS), hydroxypropylmethylcellulose phthalate (HP-55, HP-50) and methacrylic acid ethylacrylate copolymer (Eudragit L100-55) together with nevirapine as model drug were used for the preparation of solid dispersions by hot-melt extrusion. We were able to generate solid dispersions without crystalline residuals. The resulting solid dispersions were further tested for stability and dissolution performance applying two different pH-shift experiments (non-sink conditions), to simulate standard and altered gastric conditions. Solid dispersions made of enteric polymers were independent to gastric pH variability and exhibited superior dissolution performances compared to their respective physical mixtures and neat nevirapine.

Development, manufacture and characterization of niosomes for the delivery for nevirapine.

Nevirapine (NVP), used for the treatment of HIV/AIDS, exhibits unpredictable oral bioavailability, has a poor side effect profile and requires frequent dosing. Niosomes are novel drug delivery systems that have the potential to overcome these challenges. A thin layer hydration approach was used to produce niosomes and optimisation was undertaken using design of experiments (DoE) and response surface methodology (RSM) establish and identify parameters that may affect the manufacture of niosomes. The impact of cholesterol and surfactant content, hydration time and temperature on manufacture was investigated. Critical quality attributes (CQA) in respect of particle size (PS), entrapment efficiency (EE), polydispersity index (PDI) and the amount of NVP released at 48 hours was also assessed. The optimised niosome composition was identified and manufactured and the CQA characterised prior to placing the batch on stability for 12 weeks at 4±2 °C and 22±2 °C. The PS, PDI, EE and % NVP released at 48 h was 523.36±23.16 nm, 0.386±0.054, 96.8 % and 25.3 % for niosomes manufactured with Span® 20. Similarly, the parameters were 502.87±21.77 nm and 0.394±0.027, 98.0 % and 25.0 % for mean PS, PDI, EE and %NVP released at 48 h for Span® 80 niosomes. All characterisation was undertaken on the day of manufacture. In conclusion, a simple, cheap, rapid and precise method of manufacture of NVP niosomes was developed, validated and optimised using DoE and RSM and the product exhibited the target CQA.

Discovery of potent HIV-1 non-nucleoside reverse transcriptase inhibitors by exploring the structure-activity relationship of solvent-exposed regions I.

Two novel series of human immunodeficiency virus-1 (HIV-1) non-nucleoside reverse transcriptase inhibitors (NNRTIs) bearing a thiophene[3,2-d]pyrimidine scaffold and sulfonamide linker in the right wing have been identified, which demonstrated activity against the wild-type (WT) HIV-1 strain in MT-4 cells with inhibitory concentrations ranging from micromolar to submicromolar. Especially, against the mutant strains K103N and E138K, most compounds exhibited more potent activity than against WT HIV-1. Compound 7 (EC50  = 0.014, 0.031 µM) achieved the most potent activity against the two mutants, being more effective than that of nevirapine (NVP, EC50  = 7.572, 0.190 µM) and comparable to that of etravirine (ETV, EC50  = 0.004, 0.014 µM). Molecular docking experiments on the novel analogs have also suggested that the extensive network of main chain hydrogen bonds are important in the binding mode, which may provide valuable insights for further optimization.

Preparation of a highly stable drug carrier by efficient immobilization of human serum albumin (HSA) on drug-loaded magnetic iron oxide nanoparticles.

Albumin immobilized nanoparticles are known to be biodegradable, easy to prepare and reproducible for drug delivery systems. In summary, we have synthesized a new drug carrier using modified iron oxide nanoparticles. The synthesized drug carrier was characterized by X-ray powder diffraction (XRD), field-emission scanning electron microscopy (FE-SEM), Fourier transform infrared (FT-IR), vibrating sample magnetometry (VSM) and energy-dispersive X-ray spectroscopy (EDX). Three different drugs were loaded on the modified iron oxide nanoparticles and then human serum albumin (HSA) immobilized on the iron oxide nanoparticles. In addition, the in-vitro antiproliferative activity of Fe3O4@SiO2@Nev@HSA nanoparticles against Hela cancer cell line using MTT colourimetric assay was compared with nevirapine. The results show that Fe3O4@SiO2@Nev@HSA nanoparticles in comparison to nevirapine itself have more effective antiproliferative activity on Hela cancer cell lines. The IC50 value for Fe3O4@SiO2@Nev@HSA nanoparticles was 59.20 µg/ml, which is close to the antiproliferative activity of anti-cancer gefitinib with IC50 value of 76.24 µg/ml. Moreover, in vitro calf thymus DNA (ct-DNA) binding studies were investigated by various spectroscopy techniques.

Improving antiproliferative effect of the nevirapine on Hela cells by loading onto chitosan coated magnetic nanoparticles as a fully biocompatible nano drug carrier.

The freshly prepared magnetic iron oxide nanoparticles (MIONPs) were coated with SiO2 and then modified with a Si-based linker (SiL) having chlorine atom at the end of its chain. The resulting chlorine functionalized MIONPs were bonded to chitosan (CT) in trimethylamine solution. Then nevirapine (Nev) drug was loaded into above CT-SiL-MIONPs system and resulting Nev-loaded magnetic nanoparticles, Nev@CT-SiL-MIONPs, studied using different techniques. Furthermore, the value of Nev loading efficiency and also controlled delivery effect of Nev@CT-SiL-MIONP particles was determined by UV-vis spectrometer. Interestingly, the above nanomaterial showed a superparamagnetic property with a saturation magnetization value of 35.66 emu/g, indicating that it has an excellent potential application in the treatment of cancer using magnetic targeting drug delivery technology. Furthermore, the in-vitro antiproliferative activity of Nev@CT-SiL-MIONPs against cancer cell line (Hela) was compared with nevirapine using MTT colourimetric assay. The Nev-loaded magnetic nanoparticles were shown to be more effective antiproliferative on Hela cancer cell lines than nevirapine itself. Moreover, in vitro ct-DNA binding studies were investigated by UV-Vis and competitive fluorescence spectroscopies. The results showed that DNA aggregated on Nev-loaded nanoparticles via groove binding mode.

Interaction of Nevirapine with the Peptide Binding Groove of HLA-DRB1*01:01 and Its Effect on the Conformation of HLA-Peptide Complex.

Human leukocyte antigen (HLA)-DRB1*01:01 has been shown to be involved in nevirapine-induced hepatic hypersensitivity reactions. In the present study, in silico docking simulations and molecular dynamics simulations were performed to predict the interaction mode of nevirapine with the peptide binding groove of HLA-DRB1*01:01 and its possible effect on the position and orientation of the ligand peptide derived from hemagglutinin (HA). In silico analyses suggested that nevirapine interacts with HLA-DRB1*01:01 around the P4 pocket within the peptide binding groove and the HA peptide stably binds on top of nevirapine at the groove. The analyses also showed that binding of nevirapine at the groove will significantly change the inter-helical distances of the groove. An in vitro competitive assay showed that nevirapine (1000 µM) increases the binding of the HA peptide to HLA-DRB1*01:01 in an allele-specific manner. These results indicate that nevirapine might interact directly with the P4 pocket and modifies its structure, which could change the orientation of loaded peptides and the conformation of HLA-DRB1*01:01; these changes could be distinctively recognized by T-cell receptors. Through this molecular mechanism, nevirapine might stimulate the immune system, resulting in hepatic hypersensitivity reactions.

Nevirapine-polycaprolactone crystalline inclusion complex as a potential long-acting injectable solid form.

Nevirapine (NVP) is recommended by WHO as the antiretroviral treatment to prevent HIV passing from mother to child. However, the once-daily oral administration results in poor patient compliance, and a long-acting injectable form of NVP is desirable. Using single-crystal X-ray diffraction and other characterization methods, we demonstrated NVP can form crystalline inclusion complex (IC) with the biodegradable hydrophobic poly(ε-caprolactone) (PCL), and investigated the potential of the NVP-PCL IC microparticles as a long-acting injectable solid form. Compared with pure NVP crystals and NVP/polylactide microparticles, the NVP-PCL IC crystals showed significantly decreased solubility and slower dissolution rate, making it more suitable to be developed to achieve sustained-release profiles. In addition, the NVP-PCL IC microparticles with an average diameter below 10 µm can be conveniently prepared by spray drying and are found to be easily injectable through a 25G needle. These results demonstrated the possibility of using drug-polymer IC microparticles as long-acting injectable forms, providing a new approach to design sustained-release drug products.

The HIV-1 p66 homodimeric RT exhibits different conformations in the binding-competent and -incompetent NNRTI site.

Non-nucleoside inhibitors of human immunodeficiency virus type 1 reverse transcriptase (RT), NNRTIs, which bind to the p66/p51 heterodimeric RT, also interact with the p66/p66 homodimer, whose structure is unknown. 19 F nuclear magnetic resonance of a single 4-trifluoromethylphenylalanine (tfmF) residue, incorporated into the NNRTI binding pocket of the p66/p66 homodimer at position 181, was used to investigate NNRTI binding. In the NNRTI-bound homodimer complex, two different 19 F signals are observed, with the resonance frequencies matching those of the NNRTI-bound p66/p51 heterodimer spectra, in which the individual p66-subunit or p51-subunit were labeled with tfmF at positions 181. These data suggest that the NNRTI-bound p66/p66 homodimer conformation, particularly around residue 181, is very similar to that in the p66/p51 heterodimer, explaining why NNRTI binding to p66/p66 enhances dimer formation.

Spectroscopic and molecular docking studies on the interaction of antiviral drug nevirapine with calf thymus DNA.

The interaction of calf thymus DNA with nevirapine at physiological pH was studied by using absorption, circular dichroism, viscosity, differential pulse voltammetry, fluorescence techniques, salt effect studies and computational methods. The drug binds to ct-DNA in a groove binding mode, as shown by slight variation in the viscosity of ct-DNA. Furthermore, competitive fluorimetric studies with Hoechst 33258 indicate that nevirapine binds to DNA via groove binding. Moreover, the structure of nevirapine was optimized by DFT calculations and was used for the molecular docking calculations. The molecular docking results suggested that nevirapine prefers to bind on the minor groove of ct-DNA.

Cocrystal solubility product analysis - Dual concentration-pH mass action model not dependent on explicit solubility equations.

A novel general computational approach is described to address many aspects of cocrystal (CC) solubility product (Ksp) determination of drug substances. The CC analysis program, pDISOL-X, was developed and validated with published model systems of various acid-base combinations of active pharmaceutical ingredients (APIs) and coformers: (i) carbamazepine cocrystal systems with 4-aminobenzoic acid, cinnamic acid, saccharin, and salicylic acid, (ii) for indomethacin with saccharin, (iii) for nevirapine with maleic acid, saccharin, and salicylic acid, and (iv) for gabapentin with 3-hydroxybenzoic acid. In all systems but gabapentin, the coformer is much more soluble than the API. The model systems selected are those with available published dual concentration-pH data, one set for the API and one set for the coformer, generally measured at eutectic points (thermodynamically-stable three phases: solution, cocrystal, and crystalline API or coformer). The carbamazepine-cinnamic acid CC showed a substantial elevation in the API equilibrium concentration above pH5, consistent with the formation of a complex between carbamazepine and cinnamate anion. The analysis of the gabapentin:3-hydroxybenzoic acid 1:1 CC system indicated four zones of solid suspensions: coformer (pH<3.25), coformer and cocrystal eutectic (pH3.25-4.44), cocrystal (pH4.44-5.62), and API (pH>5.62). The general approach allows for testing of many possible equilibrium models, including those comprising drug-coformer complexation. The program calculates the ionic strength at each pH. From this, the equilibrium constants are adjusted for activity effects, based on the Stokes-Robinson hydration theory. The complete speciation analysis of the CC systems may provide useful insights into pH-sensitive dissolution effects that could potentially influence bioavailability.

Drug resistance-related mutations T369V/I in the connection subdomain of HIV-1 reverse transcriptase severely impair viral fitness.

Fitness is a key parameter in the measurement of transmission capacity of individual drug-resistant HIV. Drug-resistance related mutations (DRMs) T369V/I and A371V in the connection subdomain (CN) of reverse transcriptase (RT) occur at higher frequencies in the individuals experiencing antiretroviral therapy failure. Here, we evaluated the effects of T369V/I and A371V on viral fitness, in the presence or in the absence of thymidine analogue resistance-associated mutations (TAMs) and assessed the effect of potential RT structure-related mechanism on change in viral fitness. Mutations T369V/I, A371V, alone or in combination with TAMs were introduced into a modified HIV-1 infectious clone AT1 by site-directed mutagenesis. Then, experiments on mutant and wild-type virus AT2 were performed separately using a growth-competition assay, and then the relative fitness was calculated. Structural analysis of RT was conducted using Pymol software. Results showed that T369V/I severely impaired the relative virus fitness, and A371V compensated for the viral fitness reduction caused by TAMs. Structural modeling of RT suggests that T369V/I substitutions disrupt powerful hydrogen bonds formed by T369 and V365 in p51 and p66. This study indicates that the secondary DRMs within CN might efficiently damage viral fitness, and provides valuable information for clinical surveillance and prevention of HIV-1 strains carrying these DRMs.

In situ hybrid nano drug delivery system (IHN-DDS) of antiretroviral drug for simultaneous targeting to multiple viral reservoirs: An in vivo proof of concept.

We report In situ hybrid nano drug delivery system (IHN-DDS) of nevirapine (NVP) for simultaneous targeting to multiple viral reservoirs. The IHN-DDS system was comprised of a preconcentrate containing NVP, lipid, and a surfactant which when diluted with water resulted in the formation of nanoparticles of size range varied from 70 to 1100nm. Transmission electron microscopy and small angle neutron scattering studies of pellet and supernatant obtained after centrifugation of the IHN-DDS revealed spherical shaped nanoparticles and assembled structures, respectively. Uniform distribution of the NVP in lipid nanoparticles was confirmed by fourier transform infrared spectroscopy. Biodistribution studies in rats showed significant enhancement of NVP concentration of about 6.1, 5.8 and 3.7 fold in the liver, spleen, and brain, respectively after intravenous administration of IHN-DDS systems compared to plain NVP solution. In conclusion, IHN-DDS systems could be a promising approach for simultaneous multisite targeting and could provide therapeutic benefits in complete eradication of HIV infections.

Improving the solubility of nevirapine using A hydrotropy and mixed hydrotropy based solid dispersion approach.

BACKGROUND: Nevirapine, an antiviral drug, is a potent reverse transcriptase inhibitor (NNRTI). It is used in combination with nucleoside analogues for treatment of HIV type-1 (HIV-1) infection and AIDS. Nevirapine is a BCS class II drug which shows dissolution rate limited absorption. OBJECTIVES: The aim of the present research was to provide a fast dissolving solid dispersion of nevirapine. MATERIAL AND METHODS: The solubility of nevirapine was initially determined individually in four hydrotropic agents - namely urea, lactose, citric acid and mannitol - at a concentration of 10, 20, 30 and 40% w/v solutions using purified water as a solvent. The highest solubility was obtained in the 40% citric acid solution. Then different combinations of 2 and 3 hydrotropic agents in different ratios were used to determine solubility, so that the total concentration of hydrotropic agents was always 40%. RESULTS: The highest solubility was obtained in a solution of lactose and citric acid at the optimum ratio of 15:25. This optimized combination was utilized in preparing solid dispersions by a common solvent technique using distilled water as a solvent. The solid dispersions were evaluated for XRD, DSC and FTIR to show no drug-hydrotrope interaction. CONCLUSIONS: It was concluded that the concept of mixed hydrotropic solid dispersion is a safe, novel and cost-effective technique for enhancing the bioavailability of poorly water-soluble drugs by dissolving the drug in a nonionized form. The enhancement in solubility of nevirapine using hydrotropy is a clear indication of its potential to be used in the future for other poorly water-soluble drugs in which low bioavailability is a major concern.

Crystal form conversion of nevirapine solvates subjected to elevated temperature and humidity: a qualitative study.

Some known nevirapine solvates have been reported to undergo solvent exchange in aqueous media to form a stable hemihydrate. This study aimed to determine the effects of atmospheric moisture on said nevirapine solvates and to gain insight into which factors determine the end product of transformation. Solvates were prepared by solvent recrystallisation and stored, together with the anhydrous and hemihydrate forms, in a climate chamber at 40 °C and 75% RH for a period of 28 days. Samples were analyzed using DSC, TGA, FT-IR, PXRD and Karl Fischer titration. Some solvates were observed to undergo desolvation to the anhydrous form of nevirapine (Form I), whilst others converted to the hemihydrate. It was found that water miscibility of the guest solvent determined the stable form of nevirapine, anhydrous or hemihydrate, to which each solvate eventually transformed. Transformation to the hemihydrate only occurred if the guest solvent was sufficiently water soluble to allow water molecules to enter solvent channels and displace the original guest. Solvates with hydrophobic guests desolvated to the anhydrous form. We concluded that, in the absence of a guest, solvent channels are lost during transformation to the monoclinic crystal system and space group P21/c (Form I) so that water cannot enter after desolvation.